1. This study investigated the net disappearance of crude protein (CP) and amino acids (AA) from soybean meal and rapeseed meal in different sub-sections of the ileum of hens. A basal diet was used and in another 4 diets, maize starch contained in the basal diet was replaced with soybean meal or rapeseed meal at 140 and 280 g/kg so that changes in dietary AA concentrations resulted from the oilseed meals only. 2. A total of 250 Lohmann Brown pullets were used for this experiment at 20 weeks old and given one of the 5 diets for 7 d. The section between Meckel's diverticulum and 2 cm anterior to the ileo-caecal-colonic junction was taken after slaughtering the hens and cut into three sub-sections of equal length. Digesta were taken separately from each sub-section and then frozen. Net disappearance of AA and CP for the diets and the two protein sources was calculated based on standard equations and using a multiple linear regression approach. 3. Net disappearances of CP and all AA were significantly lower in the proximal sub-section than in the central and terminal sub-sections. Also, the net disappearance of CP and all AA from rapeseed meal was significantly lower in the proximal sub-section than in the central or terminal sub-sections. For soybean meal, only the net disappearances of arginine, aspartic acid, glutamic acid and phenylalanine were significantly lower in the proximal than in the terminal sub-section. No significant differences in the net disappearance of CP and AA were detected between protein sources within the central and terminal sub-sections or between the central and terminal sub-section within each protein source. Soybean meal had a significantly higher net disappearance of CP and AA (with the exception of cystine and methionine) than rapeseed meal in the proximal sub-section but these differences were not statistically significant in the central and terminal sub-sections. 4. Amino acids disappeared from the proximal region of the ileum. This needs consideration in standard approaches that are used for measuring AA digestibility. There is a variation in AA digestibility between soybean meal and rapeseed meal. The ranking of individual AA regarding their digestibility is different between the two oilseed meals.